autoanalyzeCommands -added new ADanalyze_showBindingSite command as Analyze->Dockings->Visualize Docking in context This display uses (1)spheres centered on atoms in closer-than-vdw-radii contact (2)hydrogen bonds and (3)sections of secondary structure (for sequences of 5 or more adjacent residues in the receptor with atoms close to the ligand) to show the bound ligand in the context of surrounding receptor. autoflexCommands -add explicit warning to caution users that the molecule used to calculate autogrids for AD4 should contain only the non-moving or 'rigid' residues. ConfPlayer -added support for updating the 'BindingSite' display -added support for showing information about singleton clusters -added PopulationPlayer class DlgParser: -added support for parsing the amount of time involved in the calculation -added support for parsing populations which are written when outlev is set to 4 in the AD4 dpf. DockingParameters: -added support for reorient keyword (AD4) -added dpf_written_filename attribute GridParameters: -added gpf_written_filename attribute

Added Web Services commands accessible from Run->Web Services. Registered users can now run AutoGrid and AutoDock installed on NBCR cluster.

atomTypeTools -fixed problem which sometimes occurred in merging nphs. Previously hydrogens not bonded to anything raised an exception. Now the code checks for the existence of bonds before referencing hydrogens' bonds... NB: now non-bonded hydrogens will not raise an error.

Utilities24: prepare_receptor4 -corrected initialization of 'cleanup' on line 70 to match documentation string -improved support for preserving the input atom charge on a specified type to AD4ReceptorPreparation -fixed bug where 'charges_to_add' was not initialized in some cases... summarize_docking_directory.py -new script which reads in all the docking logs in a directory into a single Docking. It clusters the results and outputs a comma-separated list showing number of conformations, number of tors, number of atoms, number of clusters, rmstol used for clustering, energy, etc. By default uses c2-specific getRMSD_custom method (line 176) which should be commented out if not appropriate. summarize_time.py -new script which reads in all the docking logs in a directory and outputs the total amount of time taken.

PMV:

- New dashboard widget showing a tree representation of molecules and allowing to rapidly execute PMV commands on molecular fragments - New Grid3D commands for rendering 3D Grids. Supports adding and removing grids to Pmv. Grid a show in a table widget used for navigating between grids. Isocontours and orthogonal slices can be computed and displayed. - New Update command under the Help menu allows the user to update Pmv with the latest version of the tools. - New Register button in the About dialog allows a user to register anytime - New BugReport Command to helpCommands. This command is for submitting bugs to Bugzila DataBase from Pmv. - New command for reading and playing GROMACS trajectory files(.trr , .xtc formats) - A new check button in the GUI of the display Sticks and balls command enable licorice representation - A new cartoon outlines rendering mode is available and can be turned on through a button on the button bar. - New 3D labels allow for more fonts, arbitrary sizes, and optional billboarding - Setting the sphere quality to 0 in display CPK or Sticks And Balls no adapts the sphere quality based on the number of displayed atoms.